PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Possible eucynodont (Synapsida: Cynodontia) tracks from a lacustrine facies in the Lower Jurassic Moenave Formation of southwestern Utah
items: The effects of occupational disruption during COVID-19 lockdowns on health: a cross-sectional study
items: Shoulder mobility and strength impairments in patients with rotator cuff related shoulder pain: a systematic review and meta analysis
items: The association between antiphospholipid syndrome and atrial fibrillation: a single center retrospective case-control study
items: Exploring the plasmodesmata callose-binding protein gene family in upland cotton: unraveling insights for enhancing fiber length
items: Novel roles of κ-opioid receptor in myocardial ischemia-reperfusion injury
items: Recovery of deep-sea meiofauna community in Kaikōura Canyon following an earthquake-triggered turbidity flow
items: TIN-X version 3: update with expanded dataset and modernized architecture for enhanced illumination of understudied targets
items: Structured peer review: pilot results from 23 Elsevier journals
items: Development and validation of a multi-parameter nomogram for venous thromboembolism in gastric cancer patients: a retrospective analysis

Possible eucynodont (Synapsida: Cynodontia) tracks from a lacustrine facies in the Lower Jurassic Moenave Formation of southwestern Utah
type: item
type: AcademicArticle
description: Eight fossil tetrapod footprints from lake-shore deposits in the Lower Jurassic Moenave Formation at the St. George Dinosaur Discovery Site (SGDS) in southwestern Utah cannot be assigned to the prevalent dinosaurian (Anomoepus, Eubrontes, Gigandipus, Grallator, Kayentapus) or crocodyliform (Batrachopus) ichnotaxa at the site. The tridactyl and tetradactyl footprints are incomplete, consisting of digit- and digit-tip-only imprints. Seven of the eight are likely pes prints; the remaining specimen is a possible manus print. The pes prints have digit imprint morphologies and similar anterior projections and divarication angles to those of Brasilichnium, an ichnotaxon found primarily in eolian paleoenvironments attributed to eucynodont synapsids. Although their incompleteness prevents clear referral to Brasilichnium, the SGDS tracks nevertheless suggest a eucynodont track maker and thus represent a rare, Early Mesozoic occurrence of such tracks outside of an eolian paleoenvironment.
format: application/pdf
format: text/html
creator: Holly Hurtado
creator: Jerald D. Harris
creator: Andrew R.C. Milner
subject: Animal Behavior
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.17591
publisher: PeerJ Inc.
rights: © 2024 Hurtado et al.
abstract: Eight fossil tetrapod footprints from lake-shore deposits in the Lower Jurassic Moenave Formation at the St. George Dinosaur Discovery Site (SGDS) in southwestern Utah cannot be assigned to the prevalent dinosaurian (Anomoepus, Eubrontes, Gigandipus, Grallator, Kayentapus) or crocodyliform (Batrachopus) ichnotaxa at the site. The tridactyl and tetradactyl footprints are incomplete, consisting of digit- and digit-tip-only imprints. Seven of the eight are likely pes prints; the remaining specimen is a possible manus print. The pes prints have digit imprint morphologies and similar anterior projections and divarication angles to those of Brasilichnium, an ichnotaxon found primarily in eolian paleoenvironments attributed to eucynodont synapsids. Although their incompleteness prevents clear referral to Brasilichnium, the SGDS tracks nevertheless suggest a eucynodont track maker and thus represent a rare, Early Mesozoic occurrence of such tracks outside of an eolian paleoenvironment.
bibliographic citation: Hurtado et al. (2024) Possible eucynodont (Synapsida: Cynodontia) tracks from a lacustrine facies in the Lower Jurassic Moenave Formation of southwestern Utah. PeerJ 12:e17591 https://doi.org/10.7717/peerj.17591
date submitted: 2023-07-24
date accepted: 2024-05-28
issued: 2024-06-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hurtado
  given name: Holly
author list: Agent
  family name: Harris
  given name: Jerald D.
author list: Agent
  family name: Milner
  given name: Andrew R.C.
doi: 10.7717/peerj.17591
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-26
copyright: ©2024 Hurtado et al.
attribution name: Hurtado et al.

The effects of occupational disruption during COVID-19 lockdowns on health: a cross-sectional study
type: item
type: AcademicArticle
description: The disruption in daily activity performance during COVID-19 lockdowns is widely understood to have impacted health, but a better understanding of how restricted performance of specific activities are associated with health is needed. This cross-sectional study answers the following question: How were changes in the performance of 16 daily activities associated with health during COVID-19 lockdowns? A total of 116 participants completed an online survey rating their health before and during COVID-19 lockdowns and comparing their recollection of the performance of 16 activities before COVID-19 with their performance during lockdowns. Multiple stepwise linear regression analysis was used to estimate the relationship between self-reported changes in activities during lockdowns and concurrent (during-lockdown) health status, while controlling for pre-COVID-19 health status. Only changes in activities that were uniquely and significantly associated with lockdown health status were retained in the final model. Health before COVID-19 accounted for 3.7% (P = 0.039) of the variance in health during COVID-19 lockdowns. After controlling for health before COVID-19, five types of activity were significantly and uniquely predictive of health during lockdowns, together accounting for 48.3% of the variance. These activities and the variances they accounted for were rest and sleep (29.5%, P < 0.001), play and recreational activities (8%, P < 0.001), work (4.8%, P = 0.002), personal hygiene (3.2%, P = 0.01), and healthy eating (2.8%, P = 0.013). The study suggests that these five types of activity should be prioritized in policy or interventions when participation in activity is constrained by lockdowns or comparable factors.
format: application/pdf
format: text/html
creator: Bernard Austin Kigunda Muriithi
creator: R. Curtis Bay
subject: Epidemiology
subject: Psychiatry and Psychology
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.17594
publisher: PeerJ Inc.
rights: © 2024 Muriithi and Bay
abstract: The disruption in daily activity performance during COVID-19 lockdowns is widely understood to have impacted health, but a better understanding of how restricted performance of specific activities are associated with health is needed. This cross-sectional study answers the following question: How were changes in the performance of 16 daily activities associated with health during COVID-19 lockdowns? A total of 116 participants completed an online survey rating their health before and during COVID-19 lockdowns and comparing their recollection of the performance of 16 activities before COVID-19 with their performance during lockdowns. Multiple stepwise linear regression analysis was used to estimate the relationship between self-reported changes in activities during lockdowns and concurrent (during-lockdown) health status, while controlling for pre-COVID-19 health status. Only changes in activities that were uniquely and significantly associated with lockdown health status were retained in the final model. Health before COVID-19 accounted for 3.7% (P = 0.039) of the variance in health during COVID-19 lockdowns. After controlling for health before COVID-19, five types of activity were significantly and uniquely predictive of health during lockdowns, together accounting for 48.3% of the variance. These activities and the variances they accounted for were rest and sleep (29.5%, P < 0.001), play and recreational activities (8%, P < 0.001), work (4.8%, P = 0.002), personal hygiene (3.2%, P = 0.01), and healthy eating (2.8%, P = 0.013). The study suggests that these five types of activity should be prioritized in policy or interventions when participation in activity is constrained by lockdowns or comparable factors.
bibliographic citation: Muriithi et al. (2024) The effects of occupational disruption during COVID-19 lockdowns on health: a cross-sectional study. PeerJ 12:e17594 https://doi.org/10.7717/peerj.17594
date submitted: 2023-12-22
date accepted: 2024-05-28
issued: 2024-06-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Muriithi
  given name: Bernard Austin Kigunda
author list: Agent
  family name: Bay
  given name: R. Curtis
doi: 10.7717/peerj.17594
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-26
copyright: ©2024 Muriithi and Bay
attribution name: Muriithi and Bay

Shoulder mobility and strength impairments in patients with rotator cuff related shoulder pain: a systematic review and meta analysis
type: item
type: AcademicArticle
description: Background The methods previously proposed in the literature to assess patients with rotator cuff related shoulder pain, based on special orthopedic tests to precisely identify the structure causing the shoulder symptoms have been recently challenged. This opens the possibility of a different way of physical examination. Objective To analyze the differences in shoulder range of motion, strength and thoracic kyphosis between rotator cuff related shoulder pain patients and an asymptomatic group. Method The protocol of the present research was registered in the International Prospective Register of Systematic Review (PROSPERO) (registration number CRD42021258924). Database search of observational studies was conducted in MEDLINE, EMBASE, WOS and CINHAL until July 2023, which assessed shoulder or neck neuro-musculoskeletal non-invasive physical examination compared to an asymptomatic group. Two investigators assessed eligibility and study quality. The Newcastle Ottawa Scale was used to evaluate the methodology quality. Results Eight studies (N = 604) were selected for the quantitative analysis. Meta-analysis showed statistical differences with large effect for shoulder flexion (I2 = 91.7%, p < 0.01, HG = −1.30), external rotation (I2 = 83.2%, p < 0.01, HG = −1.16) and internal rotation range of motion (I2 = 0%, p < 0.01, HG = −1.32). Regarding to shoulder strength; only internal rotation strength showed statistical differences with small effect (I2 = 42.8%, p < 0.05, HG = −0.3). Conclusions There is moderate to strong evidence that patients with rotator cuff related shoulder pain present less shoulder flexion, internal and external rotation range of motion and less internal rotation strength than asymptomatic individuals.
format: application/pdf
format: text/html
creator: Daniel Manoso-Hernando
creator: Javier Bailón-Cerezo
creator: Santiago Angulo-Díaz-Parreño
creator: Álvaro Reina-Varona
creator: Ignacio Elizagaray-García
creator: Alfonso Gil-Martínez
subject: Anesthesiology and Pain Management
subject: Kinesiology
subject: Orthopedics
subject: Biomechanics
subject: Rehabilitation
description: doi:10.7717/peerj.17604
publisher: PeerJ Inc.
rights: © 2024 Manoso-Hernando et al.
abstract: Background The methods previously proposed in the literature to assess patients with rotator cuff related shoulder pain, based on special orthopedic tests to precisely identify the structure causing the shoulder symptoms have been recently challenged. This opens the possibility of a different way of physical examination. Objective To analyze the differences in shoulder range of motion, strength and thoracic kyphosis between rotator cuff related shoulder pain patients and an asymptomatic group. Method The protocol of the present research was registered in the International Prospective Register of Systematic Review (PROSPERO) (registration number CRD42021258924). Database search of observational studies was conducted in MEDLINE, EMBASE, WOS and CINHAL until July 2023, which assessed shoulder or neck neuro-musculoskeletal non-invasive physical examination compared to an asymptomatic group. Two investigators assessed eligibility and study quality. The Newcastle Ottawa Scale was used to evaluate the methodology quality. Results Eight studies (N = 604) were selected for the quantitative analysis. Meta-analysis showed statistical differences with large effect for shoulder flexion (I2 = 91.7%, p < 0.01, HG = −1.30), external rotation (I2 = 83.2%, p < 0.01, HG = −1.16) and internal rotation range of motion (I2 = 0%, p < 0.01, HG = −1.32). Regarding to shoulder strength; only internal rotation strength showed statistical differences with small effect (I2 = 42.8%, p < 0.05, HG = −0.3). Conclusions There is moderate to strong evidence that patients with rotator cuff related shoulder pain present less shoulder flexion, internal and external rotation range of motion and less internal rotation strength than asymptomatic individuals.
bibliographic citation: Manoso-Hernando et al. (2024) Shoulder mobility and strength impairments in patients with rotator cuff related shoulder pain: a systematic review and meta analysis. PeerJ 12:e17604 https://doi.org/10.7717/peerj.17604
date submitted: 2024-01-15
date accepted: 2024-05-30
issued: 2024-06-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Manoso-Hernando
  given name: Daniel
author list: Agent
  family name: Bailón-Cerezo
  given name: Javier
author list: Agent
  family name: Angulo-Díaz-Parreño
  given name: Santiago
author list: Agent
  family name: Reina-Varona
  given name: Álvaro
author list: Agent
  family name: Elizagaray-García
  given name: Ignacio
author list: Agent
  family name: Gil-Martínez
  given name: Alfonso
doi: 10.7717/peerj.17604
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-26
copyright: ©2024 Manoso-Hernando et al.
attribution name: Manoso-Hernando et al.

The association between antiphospholipid syndrome and atrial fibrillation: a single center retrospective case-control study
type: item
type: AcademicArticle
description: Antiphospholipid syndrome (APS) is a systemic autoimmune syndrome characterized by arterial or venous thrombosis, pregnancy complications and thrombocytopenia. The aim of this study is to investigate the association between APS and atrial fibrillation (AF) among patients in Peking University People’s Hospital. A single center retrospective study was conducted. Cases were hospitalized patients diagnosed with AF by a cardiologist while the control group patients did not exhibit cardiac diseases. The results of the study revealed that in multivariable logistic regression, APS, anticardiolipin antibody (aCL) positivity and anti-beta-2-glycoprotein antibody (anti-β2GPI) positivity are independent risk factors of AF. APS, aCL positivity and anti-β2GPI positivity are statistically different between AF patients and non-AF patients. Forthcoming studies are needed to clarify the potential link between APS and AF.
format: application/pdf
format: text/html
creator: Zechuan Zhou
creator: Yuansheng Liu
subject: Allergy and Clinical Immunology
subject: Cardiology
subject: Immunology
subject: Internal Medicine
subject: Rheumatology
description: doi:10.7717/peerj.17617
publisher: PeerJ Inc.
rights: © 2024 Zhou and Liu
abstract: Antiphospholipid syndrome (APS) is a systemic autoimmune syndrome characterized by arterial or venous thrombosis, pregnancy complications and thrombocytopenia. The aim of this study is to investigate the association between APS and atrial fibrillation (AF) among patients in Peking University People’s Hospital. A single center retrospective study was conducted. Cases were hospitalized patients diagnosed with AF by a cardiologist while the control group patients did not exhibit cardiac diseases. The results of the study revealed that in multivariable logistic regression, APS, anticardiolipin antibody (aCL) positivity and anti-beta-2-glycoprotein antibody (anti-β2GPI) positivity are independent risk factors of AF. APS, aCL positivity and anti-β2GPI positivity are statistically different between AF patients and non-AF patients. Forthcoming studies are needed to clarify the potential link between APS and AF.
bibliographic citation: Zhou et al. (2024) The association between antiphospholipid syndrome and atrial fibrillation: a single center retrospective case-control study. PeerJ 12:e17617 https://doi.org/10.7717/peerj.17617
date submitted: 2024-04-01
date accepted: 2024-05-31
issued: 2024-06-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Zechuan
author list: Agent
  family name: Liu
  given name: Yuansheng
doi: 10.7717/peerj.17617
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-26
copyright: ©2024 Zhou and Liu
attribution name: Zhou and Liu

Exploring the plasmodesmata callose-binding protein gene family in upland cotton: unraveling insights for enhancing fiber length
type: item
type: AcademicArticle
description: Plasmodesmata are transmembrane channels embedded within the cell wall that can facilitate the intercellular communication in plants. Plasmodesmata callose-binding (PDCB) protein that associates with the plasmodesmata contributes to cell wall extension. Given that the elongation of cotton fiber cells correlates with the dynamics of the cell wall, this protein can be related to the cotton fiber elongation. This study sought to identify PDCB family members within the Gossypium. hirsutum genome and to elucidate their expression profiles. A total of 45 distinct family members were observed through the identification and screening processes. The analysis of their physicochemical properties revealed the similarity in the amino acid composition and molecular weight across most members. The phylogenetic analysis facilitated the construction of an evolutionary tree, categorizing these members into five groups mainly distributed on 20 chromosomes. The fine mapping results facilitated a tissue-specific examination of group V, revealing that the expression level of GhPDCB9 peaked five days after flowering. The VIGS experiments resulted in a marked decrease in the gene expression level and a significant reduction in the mature fiber length, averaging a shortening of 1.43–4.77 mm. The results indicated that GhPDCB9 played a pivotal role in the cotton fiber development and served as a candidate for enhancing cotton yield.
format: application/pdf
format: text/html
creator: Haibo Zhang
creator: Xianghui Xiao
creator: Ziyin Li
creator: Yu Chen
creator: Pengtao Li
creator: Renhai Peng
creator: Quanwei Lu
creator: Youwu Wang
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.17625
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Plasmodesmata are transmembrane channels embedded within the cell wall that can facilitate the intercellular communication in plants. Plasmodesmata callose-binding (PDCB) protein that associates with the plasmodesmata contributes to cell wall extension. Given that the elongation of cotton fiber cells correlates with the dynamics of the cell wall, this protein can be related to the cotton fiber elongation. This study sought to identify PDCB family members within the Gossypium. hirsutum genome and to elucidate their expression profiles. A total of 45 distinct family members were observed through the identification and screening processes. The analysis of their physicochemical properties revealed the similarity in the amino acid composition and molecular weight across most members. The phylogenetic analysis facilitated the construction of an evolutionary tree, categorizing these members into five groups mainly distributed on 20 chromosomes. The fine mapping results facilitated a tissue-specific examination of group V, revealing that the expression level of GhPDCB9 peaked five days after flowering. The VIGS experiments resulted in a marked decrease in the gene expression level and a significant reduction in the mature fiber length, averaging a shortening of 1.43–4.77 mm. The results indicated that GhPDCB9 played a pivotal role in the cotton fiber development and served as a candidate for enhancing cotton yield.
bibliographic citation: Zhang et al. (2024) Exploring the plasmodesmata callose-binding protein gene family in upland cotton: unraveling insights for enhancing fiber length. PeerJ 12:e17625 https://doi.org/10.7717/peerj.17625
date submitted: 2024-01-28
date accepted: 2024-06-02
issued: 2024-06-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Haibo
author list: Agent
  family name: Xiao
  given name: Xianghui
author list: Agent
  family name: Li
  given name: Ziyin
author list: Agent
  family name: Chen
  given name: Yu
author list: Agent
  family name: Li
  given name: Pengtao
author list: Agent
  family name: Peng
  given name: Renhai
author list: Agent
  family name: Lu
  given name: Quanwei
author list: Agent
  family name: Wang
  given name: Youwu
doi: 10.7717/peerj.17625
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-26
copyright: ©2024 Zhang et al.
attribution name: Zhang et al.

Novel roles of κ-opioid receptor in myocardial ischemia-reperfusion injury
type: item
type: AcademicArticle
description: Acute heart attack is the primary cause of cardiovascular-related death worldwide. A common treatment is reperfusion of ischemic tissue, which can cause irreversible damage to the myocardium. The number of mitochondria in cardiomyocytes is large, which generate adenosine triphosphate (ATP) to sustain proper cardiac contractile function, and mitochondrial dysfunction plays a crucial role in cell death during myocardial ischemia-reperfusion, leading to an increasing number of studies investigating the impact of mitochondria on ischemia-reperfusion injury. The disarray of mitochondrial dynamics, excessive Ca2+ accumulation, activation of mitochondrial permeable transition pores, swelling of mitochondria, ultimately the death of cardiomyocyte are the consequences of ischemia-reperfusion injury. κ-opioid receptors can alleviate mitochondrial dysfunction, regulate mitochondrial dynamics, mitigate myocardial ischemia-reperfusion injury, exert protective effects on myocardium. The mechanism of κ-OR activation during myocardial ischemia-reperfusion to regulate mitochondrial dynamics and reduce myocardial ischemia-reperfusion injury will be discussed, so as to provide theoretical basis for the protection of ischemic myocardium.
format: application/pdf
format: text/html
creator: Wen Zhang
creator: Qi Zhang
creator: Yali Liu
creator: Jianming Pei
creator: Na Feng
subject: Biochemistry
subject: Cell Biology
subject: Cardiology
description: doi:10.7717/peerj.17333
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Acute heart attack is the primary cause of cardiovascular-related death worldwide. A common treatment is reperfusion of ischemic tissue, which can cause irreversible damage to the myocardium. The number of mitochondria in cardiomyocytes is large, which generate adenosine triphosphate (ATP) to sustain proper cardiac contractile function, and mitochondrial dysfunction plays a crucial role in cell death during myocardial ischemia-reperfusion, leading to an increasing number of studies investigating the impact of mitochondria on ischemia-reperfusion injury. The disarray of mitochondrial dynamics, excessive Ca2+ accumulation, activation of mitochondrial permeable transition pores, swelling of mitochondria, ultimately the death of cardiomyocyte are the consequences of ischemia-reperfusion injury. κ-opioid receptors can alleviate mitochondrial dysfunction, regulate mitochondrial dynamics, mitigate myocardial ischemia-reperfusion injury, exert protective effects on myocardium. The mechanism of κ-OR activation during myocardial ischemia-reperfusion to regulate mitochondrial dynamics and reduce myocardial ischemia-reperfusion injury will be discussed, so as to provide theoretical basis for the protection of ischemic myocardium.
bibliographic citation: Zhang et al. (2024) Novel roles of κ-opioid receptor in myocardial ischemia-reperfusion injury. PeerJ 12:e17333 https://doi.org/10.7717/peerj.17333
date submitted: 2024-01-18
date accepted: 2024-04-12
issued: 2024-06-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Wen
author list: Agent
  family name: Zhang
  given name: Qi
author list: Agent
  family name: Liu
  given name: Yali
author list: Agent
  family name: Pei
  given name: Jianming
author list: Agent
  family name: Feng
  given name: Na
doi: 10.7717/peerj.17333
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-25
copyright: ©2024 Zhang et al.
attribution name: Zhang et al.

Recovery of deep-sea meiofauna community in Kaikōura Canyon following an earthquake-triggered turbidity flow
type: item
type: AcademicArticle
description: Turbidity flows can transport massive amounts of sediment across large distances with dramatic, long-lasting impacts on deep-sea benthic communities. The 2016 Mw 7.8 Kaikōura Earthquake triggered a canyon-flushing event in Kaikōura Canyon, New Zealand, which included significant submarine mass wasting, debris, and turbidity flows. This event provided an excellent opportunity to investigate the effects of large-scale natural disturbance on benthic ecosystems. Benthic meiofauna community structure before and after the event was analysed from a time series of sediment cores collected 10 years and 6 years before, and 10 weeks, 10 months, and 4 years after the disturbance. Immediately after the 2016 event abundances of all meiofauna dramatically decreased. Four years later the meiofauna community had recovered and was no longer distinguishable from the pre-event community. However, the nematode component of the community was similar, but not fully comparable to the pre-event community by 4 years after the disturbance. Community recovery was systematically correlated to changes in the physical characteristics of the habitat caused by the disturbance, using physical and biochemical variables derived from sediment cores, namely: sediment texture, organic matter, and pigment content. While these environmental variables explained relatively little of the overall variability in meiofauna community structure, particle size, food availability and quality were significant components. The minimum threshold time for the meiofauna community to fully recover was estimated to be between 3.9 and 4.7 years, although the predicted recovery time for the nematode community was longer, between 4.6 and 5 years. We consider the management implications of this study in comparison to the few studies of large-scale disturbances in the deep sea, in terms of their relevance to the efficacy of the marine reserve that encompasses Kaikōura Canyon, along with potential implications for our understandi…
format: application/pdf
format: text/html
creator: Katharine T. Bigham
creator: Daniel Leduc
creator: Ashley A. Rowden
creator: David A. Bowden
creator: Scott D. Nodder
creator: Alan R. Orpin
subject: Ecology
subject: Environmental Sciences
subject: Marine Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.17367
publisher: PeerJ Inc.
rights: © 2024 Bigham et al.
abstract: Turbidity flows can transport massive amounts of sediment across large distances with dramatic, long-lasting impacts on deep-sea benthic communities. The 2016 Mw 7.8 Kaikōura Earthquake triggered a canyon-flushing event in Kaikōura Canyon, New Zealand, which included significant submarine mass wasting, debris, and turbidity flows. This event provided an excellent opportunity to investigate the effects of large-scale natural disturbance on benthic ecosystems. Benthic meiofauna community structure before and after the event was analysed from a time series of sediment cores collected 10 years and 6 years before, and 10 weeks, 10 months, and 4 years after the disturbance. Immediately after the 2016 event abundances of all meiofauna dramatically decreased. Four years later the meiofauna community had recovered and was no longer distinguishable from the pre-event community. However, the nematode component of the community was similar, but not fully comparable to the pre-event community by 4 years after the disturbance. Community recovery was systematically correlated to changes in the physical characteristics of the habitat caused by the disturbance, using physical and biochemical variables derived from sediment cores, namely: sediment texture, organic matter, and pigment content. While these environmental variables explained relatively little of the overall variability in meiofauna community structure, particle size, food availability and quality were significant components. The minimum threshold time for the meiofauna community to fully recover was estimated to be between 3.9 and 4.7 years, although the predicted recovery time for the nematode community was longer, between 4.6 and 5 years. We consider the management implications of this study in comparison to the few studies of large-scale disturbances in the deep sea, in terms of their relevance to the efficacy of the marine reserve that encompasses Kaikōura Canyon, along with potential implications for our understandi…
bibliographic citation: Bigham et al. (2024) Recovery of deep-sea meiofauna community in Kaikōura Canyon following an earthquake-triggered turbidity flow. PeerJ 12:e17367 https://doi.org/10.7717/peerj.17367
date submitted: 2024-01-12
date accepted: 2024-04-18
issued: 2024-06-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bigham
  given name: Katharine T.
author list: Agent
  family name: Leduc
  given name: Daniel
author list: Agent
  family name: Rowden
  given name: Ashley A.
author list: Agent
  family name: Bowden
  given name: David A.
author list: Agent
  family name: Nodder
  given name: Scott D.
author list: Agent
  family name: Orpin
  given name: Alan R.
doi: 10.7717/peerj.17367
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-25
copyright: ©2024 Bigham et al.
attribution name: Bigham et al.

TIN-X version 3: update with expanded dataset and modernized architecture for enhanced illumination of understudied targets
type: item
type: AcademicArticle
description: TIN-X (Target Importance and Novelty eXplorer) is an interactive visualization tool for illuminating associations between diseases and potential drug targets and is publicly available at newdrugtargets.org. TIN-X uses natural language processing to identify disease and protein mentions within PubMed content using previously published tools for named entity recognition (NER) of gene/protein and disease names. Target data is obtained from the Target Central Resource Database (TCRD). Two important metrics, novelty and importance, are computed from this data and when plotted as log(importance) vs. log(novelty), aid the user in visually exploring the novelty of drug targets and their associated importance to diseases. TIN-X Version 3.0 has been significantly improved with an expanded dataset, modernized architecture including a REST API, and an improved user interface (UI). The dataset has been expanded to include not only PubMed publication titles and abstracts, but also full-text articles when available. This results in approximately 9-fold more target/disease associations compared to previous versions of TIN-X. Additionally, the TIN-X database containing this expanded dataset is now hosted in the cloud via Amazon RDS. Recent enhancements to the UI focuses on making it more intuitive for users to find diseases or drug targets of interest while providing a new, sortable table-view mode to accompany the existing plot-view mode. UI improvements also help the user browse the associated PubMed publications to explore and understand the basis of TIN-X’s predicted association between a specific disease and a target of interest. While implementing these upgrades, computational resources are balanced between the webserver and the user’s web browser to achieve adequate performance while accommodating the expanded dataset. Together, these advances aim to extend the duration that users can benefit from TIN-X while providing both an expanded dataset and new features that researcher…
format: application/pdf
format: text/html
creator: Vincent T. Metzger
creator: Daniel C. Cannon
creator: Jeremy J. Yang
creator: Stephen L. Mathias
creator: Cristian G. Bologa
creator: Anna Waller
creator: Stephan C. Schürer
creator: Dušica Vidović
creator: Keith J. Kelleher
creator: Timothy K. Sheils
creator: Lars Juhl Jensen
creator: Christophe G. Lambert
creator: Tudor I. Oprea
creator: Jeremy S. Edwards
subject: Bioinformatics
subject: Computational Biology
subject: Translational Medicine
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.17470
publisher: PeerJ Inc.
rights: © 2024 Metzger et al.
abstract: TIN-X (Target Importance and Novelty eXplorer) is an interactive visualization tool for illuminating associations between diseases and potential drug targets and is publicly available at newdrugtargets.org. TIN-X uses natural language processing to identify disease and protein mentions within PubMed content using previously published tools for named entity recognition (NER) of gene/protein and disease names. Target data is obtained from the Target Central Resource Database (TCRD). Two important metrics, novelty and importance, are computed from this data and when plotted as log(importance) vs. log(novelty), aid the user in visually exploring the novelty of drug targets and their associated importance to diseases. TIN-X Version 3.0 has been significantly improved with an expanded dataset, modernized architecture including a REST API, and an improved user interface (UI). The dataset has been expanded to include not only PubMed publication titles and abstracts, but also full-text articles when available. This results in approximately 9-fold more target/disease associations compared to previous versions of TIN-X. Additionally, the TIN-X database containing this expanded dataset is now hosted in the cloud via Amazon RDS. Recent enhancements to the UI focuses on making it more intuitive for users to find diseases or drug targets of interest while providing a new, sortable table-view mode to accompany the existing plot-view mode. UI improvements also help the user browse the associated PubMed publications to explore and understand the basis of TIN-X’s predicted association between a specific disease and a target of interest. While implementing these upgrades, computational resources are balanced between the webserver and the user’s web browser to achieve adequate performance while accommodating the expanded dataset. Together, these advances aim to extend the duration that users can benefit from TIN-X while providing both an expanded dataset and new features that researcher…
bibliographic citation: Metzger et al. (2024) TIN-X version 3: update with expanded dataset and modernized architecture for enhanced illumination of understudied targets. PeerJ 12:e17470 https://doi.org/10.7717/peerj.17470
date submitted: 2023-05-10
date accepted: 2024-05-06
issued: 2024-06-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Metzger
  given name: Vincent T.
author list: Agent
  family name: Cannon
  given name: Daniel C.
author list: Agent
  family name: Yang
  given name: Jeremy J.
author list: Agent
  family name: Mathias
  given name: Stephen L.
author list: Agent
  family name: Bologa
  given name: Cristian G.
author list: Agent
  family name: Waller
  given name: Anna
author list: Agent
  family name: Schürer
  given name: Stephan C.
author list: Agent
  family name: Vidović
  given name: Dušica
author list: Agent
  family name: Kelleher
  given name: Keith J.
author list: Agent
  family name: Sheils
  given name: Timothy K.
author list: Agent
  family name: Jensen
  given name: Lars Juhl
author list: Agent
  family name: Lambert
  given name: Christophe G.
author list: Agent
  family name: Oprea
  given name: Tudor I.
author list: Agent
  family name: Edwards
  given name: Jeremy S.
doi: 10.7717/peerj.17470
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-25
copyright: © 2024 Metzger et al.
attribution name: Metzger et al.

Structured peer review: pilot results from 23 Elsevier journals
type: item
type: AcademicArticle
description: Background Reviewers rarely comment on the same aspects of a manuscript, making it difficult to properly assess manuscripts’ quality and the quality of the peer review process. The goal of this pilot study was to evaluate structured peer review implementation by: 1) exploring whether and how reviewers answered structured peer review questions, 2) analysing reviewer agreement, 3) comparing that agreement to agreement before implementation of structured peer review, and 4) further enhancing the piloted set of structured peer review questions. Methods Structured peer review consisting of nine questions was piloted in August 2022 in 220 Elsevier journals. We randomly selected 10% of these journals across all fields and IF quartiles and included manuscripts that received two review reports in the first 2 months of the pilot, leaving us with 107 manuscripts belonging to 23 journals. Eight questions had open-ended fields, while the ninth question (on language editing) had only a yes/no option. The reviews could also leave Comments-to-Author and Comments-to-Editor. Answers were independently analysed by two raters, using qualitative methods. Results Almost all the reviewers (n = 196, 92%) provided answers to all questions even though these questions were not mandatory in the system. The longest answer (Md 27 words, IQR 11 to 68) was for reporting methods with sufficient details for replicability or reproducibility. The reviewers had the highest (partial) agreement (of 72%) for assessing the flow and structure of the manuscript, and the lowest (of 53%) for assessing whether interpretation of the results was supported by data, and for assessing whether the statistical analyses were appropriate and reported in sufficient detail (52%). Two thirds of the reviewers (n = 145, 68%) filled out the Comments-to-Author section, of which 105 (49%) resembled traditional peer review reports. These reports contained a Md of 4 (IQR 3 to 5) topics covered by the structured questions. Absolut…
format: application/pdf
format: text/html
creator: Mario Malički
creator: Bahar Mehmani
subject: Science and Medical Education
subject: Science Policy
subject: Data Science
description: doi:10.7717/peerj.17514
publisher: PeerJ Inc.
rights: © 2024 Malički and Mehmani
abstract: Background Reviewers rarely comment on the same aspects of a manuscript, making it difficult to properly assess manuscripts’ quality and the quality of the peer review process. The goal of this pilot study was to evaluate structured peer review implementation by: 1) exploring whether and how reviewers answered structured peer review questions, 2) analysing reviewer agreement, 3) comparing that agreement to agreement before implementation of structured peer review, and 4) further enhancing the piloted set of structured peer review questions. Methods Structured peer review consisting of nine questions was piloted in August 2022 in 220 Elsevier journals. We randomly selected 10% of these journals across all fields and IF quartiles and included manuscripts that received two review reports in the first 2 months of the pilot, leaving us with 107 manuscripts belonging to 23 journals. Eight questions had open-ended fields, while the ninth question (on language editing) had only a yes/no option. The reviews could also leave Comments-to-Author and Comments-to-Editor. Answers were independently analysed by two raters, using qualitative methods. Results Almost all the reviewers (n = 196, 92%) provided answers to all questions even though these questions were not mandatory in the system. The longest answer (Md 27 words, IQR 11 to 68) was for reporting methods with sufficient details for replicability or reproducibility. The reviewers had the highest (partial) agreement (of 72%) for assessing the flow and structure of the manuscript, and the lowest (of 53%) for assessing whether interpretation of the results was supported by data, and for assessing whether the statistical analyses were appropriate and reported in sufficient detail (52%). Two thirds of the reviewers (n = 145, 68%) filled out the Comments-to-Author section, of which 105 (49%) resembled traditional peer review reports. These reports contained a Md of 4 (IQR 3 to 5) topics covered by the structured questions. Absolut…
bibliographic citation: Malički et al. (2024) Structured peer review: pilot results from 23 Elsevier journals. PeerJ 12:e17514 https://doi.org/10.7717/peerj.17514
date submitted: 2024-02-08
date accepted: 2024-05-13
issued: 2024-06-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Malički
  given name: Mario
author list: Agent
  family name: Mehmani
  given name: Bahar
doi: 10.7717/peerj.17514
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-25
copyright: © 2024 Malički and Mehmani
attribution name: Malički and Mehmani

Development and validation of a multi-parameter nomogram for venous thromboembolism in gastric cancer patients: a retrospective analysis
type: item
type: AcademicArticle
description: Objective Gastric cancer (GC), one of the highest venous thromboembolism (VTE) incidence rates in cancer, contributes to considerable morbidity, mortality, and, prominently, extra cost. However, up to now, there is not a high-quality VTE model to steadily predict the risk for VTE in China. Consequently, setting up a prediction model to predict the VTE risk is imperative. Methods Data from 3,092 patients from December 15, 2017, to December 31, 2022, were retrospectively analyzed. Multiple logistic regression analysis was performed to assess risk factors for GC, and a nomogram was constructed based on screened risk factors. A receiver operating curve (ROC) and calibration plot was created to evaluate the accuracy of the nomogram. Results The risk factors of suffering from VTE were older age (OR = 1.02, 95% CI [1.00–1.04]), Karnofsky Performance Status (KPS) ≥ 70 (OR = 0.45, 95% CI [0.25–0.83]), Blood transfusion (OR = 2.37, 95% CI [1.47–3.84]), advanced clinical stage (OR = 3.98, 95% CI [1.59–9.99]), central venous catheterization (CVC) (OR = 4.27, 95% CI [2.03–8.99]), operation (OR = 2.72, 95% CI [1.55–4.77]), fibrinogen degradation product (FDP) >5 µg/mL (OR = 1.92, 95% CI [1.13–3.25]), and D-dimer > 0.5 mg/L (OR = 2.50, 95% CI [1.19–5.28]). The area under the ROC curve (AUC) was 0.82 in the training set and 0.85 in the validation set. Conclusion Our prediction model can accurately predict the risk of the appearance of VTE in gastric cancer patients and can be used as a robust and efficient tool for evaluating the possibility of VTE.
format: application/pdf
format: text/html
creator: Hang Zhou
creator: Haike Lei
creator: Huai Zhao
creator: Kaifeng Huang
creator: Yundong Wang
creator: Ruixia Hong
creator: Jishun Huo
creator: Li Luo
creator: Fang Li
subject: Cardiology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.17527
publisher: PeerJ Inc.
rights: © 2024 Zhou et al.
abstract: Objective Gastric cancer (GC), one of the highest venous thromboembolism (VTE) incidence rates in cancer, contributes to considerable morbidity, mortality, and, prominently, extra cost. However, up to now, there is not a high-quality VTE model to steadily predict the risk for VTE in China. Consequently, setting up a prediction model to predict the VTE risk is imperative. Methods Data from 3,092 patients from December 15, 2017, to December 31, 2022, were retrospectively analyzed. Multiple logistic regression analysis was performed to assess risk factors for GC, and a nomogram was constructed based on screened risk factors. A receiver operating curve (ROC) and calibration plot was created to evaluate the accuracy of the nomogram. Results The risk factors of suffering from VTE were older age (OR = 1.02, 95% CI [1.00–1.04]), Karnofsky Performance Status (KPS) ≥ 70 (OR = 0.45, 95% CI [0.25–0.83]), Blood transfusion (OR = 2.37, 95% CI [1.47–3.84]), advanced clinical stage (OR = 3.98, 95% CI [1.59–9.99]), central venous catheterization (CVC) (OR = 4.27, 95% CI [2.03–8.99]), operation (OR = 2.72, 95% CI [1.55–4.77]), fibrinogen degradation product (FDP) >5 µg/mL (OR = 1.92, 95% CI [1.13–3.25]), and D-dimer > 0.5 mg/L (OR = 2.50, 95% CI [1.19–5.28]). The area under the ROC curve (AUC) was 0.82 in the training set and 0.85 in the validation set. Conclusion Our prediction model can accurately predict the risk of the appearance of VTE in gastric cancer patients and can be used as a robust and efficient tool for evaluating the possibility of VTE.
bibliographic citation: Zhou et al. (2024) Development and validation of a multi-parameter nomogram for venous thromboembolism in gastric cancer patients: a retrospective analysis. PeerJ 12:e17527 https://doi.org/10.7717/peerj.17527
date submitted: 2023-10-31
date accepted: 2024-05-17
issued: 2024-06-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Hang
author list: Agent
  family name: Lei
  given name: Haike
author list: Agent
  family name: Zhao
  given name: Huai
author list: Agent
  family name: Huang
  given name: Kaifeng
author list: Agent
  family name: Wang
  given name: Yundong
author list: Agent
  family name: Hong
  given name: Ruixia
author list: Agent
  family name: Huo
  given name: Jishun
author list: Agent
  family name: Luo
  given name: Li
author list: Agent
  family name: Li
  given name: Fang
doi: 10.7717/peerj.17527
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-25
copyright: © 2024 Zhou et al.
attribution name: Zhou et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359